Statistical methods in interphase cytogenetics: an experimental approach

Semi-automated scoring of triple-probe FISH in human sperm using confocal microscopy

Structural and numerical sperm chromosomal aberrations result from abnormal meiosis and are directly linked to infertility. Any live births that arise from aneuploid conceptuses can result in syndromes such as Kleinfelter, Turners, XYY and Edwards. Multi-probe fluorescence in situ hybridization (FISH) is commonly used to study sperm aneuploidy, however manual FISH scoring in sperm samples is labor-intensive and introduces errors. Automated scoring methods are continuously evolving. One challenging aspect for optimizing automated sperm FISH scoring has been the overlap in excitation and emission of the fluorescent probes used to enumerate the chromosomes of interest. Our objective was to demonstrate the feasibility of combining confocal microscopy and spectral imaging with high-throughput methods for accurately measuring sperm aneuploidy. Our approach used confocal microscopy to analyze numerical chromosomal abnormalities in human sperm using enhanced slide preparation and rigorous semi-automated scoring methods. FISH for chromosomes X, Y, and 18 was conducted to determine sex chromosome disomy in sperm nuclei. Application of online spectral linear unmixing was used for effective separation of four fluorochromes while decreasing data acquisition time. Semi-automated image processing, segmentation, classification, and scoring were performed on 10 slides using custom image processing and analysis software and results were compared with manual methods. No significant differences in disomy frequencies were seen between the semi automated and manual methods. Samples treated with pepsin were observed to have reduced background autofluorescence and more uniform distribution of cells. These results demonstrate that semi-automated methods using spectral imaging on a confocal platform are a feasible approach for analyzing numerical chromosomal aberrations in sperm, and are comparable to manual methods. © 2017 International Society for Advancement of Cytometry.

State-of-the-art FISHing: automated analysis of cytogenetic aberrations in interphase nuclei

Interphase fluorescence in situ hybridization (i-FISH) is a powerful tool for visualizing various molecular targets in non-dividing cells. Manual scoring of i-FISH signals is a labor intensive, time-consuming, and error-prone process liable to subjective interpretation. Automated evaluation of signal patterns provides the opportunity to overcome these difficulties. The first report on automated i-FISH analysis has been published 20 years ago and since then several applications have been introduced in the fields of oncology, and prenatal and fertility screening. In this article, we provide an insight into the automated i-FISH analysis including its course, brief history, clinical applications, and advantages and challenges. The lack of guidelines for describing new automated i-FISH methods hampers the precise comparison of performance of various applications published, thus, we make a proposal for a panel of parameters essential to introduce and standardize new applications and reproduce previously described technologies.

Processing and staining of cell and tissue material for interphase cytogenetics

This unit describes in detail the protocols for preparation of biological specimens (fresh or fixed) for the purposes of establishing in situ hybridization procedures using probes for specific regions of the genome, allowing targeted detection of numerical and structural chromosome aberrations in the interphase nucleus. The authors present a series of comprehensive protocols from the simplest to the most complex.

Basic preparative techniques for fluorescence in situ hybridization

This unit presents protocols for preparing human metaphase chromosome slides from peripheral blood lymphocytes, isolating interphase nuclei from lymphocytes and paraffin-embedded tissues, and preparing DNA fibers. The protocols are designed so that the resulting preparations are amenable to FISH. The methods correspond to a selection of the specimens that can be analyzed with FISH techniques, and the choice of sample preparation method is highly dependent on the molecular cytogenetics question being addressed.

Automated scoring of multiprobe FISH in human spermatozoa

In the case of chromosomal aneuploidy in sperm wherein the incident rate is low and a large number of cells require scoring, automated methods that rely on computer software to segment and to count fluorescence signals are particularly necessary due to countless hours spent in reading slides and to the potential for interoperator differences. The purpose of this pilot experiment was to determine whether there were significant differences in the estimates of disomy frequency produced by automated versus manual scoring of signals for chromosome X, Y, and 18 in human sperm. The frequency of X18, Y18, XX18, YY18, and XY18 were determined in four separate normozoospermic samples. Slides were hybridized using a standard sperm FISH protocol for centromere-specific probes. Between 500 and 564, DAPI positive nuclei were captured from each sample and scored using the automated system, and the same slides were scored by a trained cytogeneticist, who was blind to the purpose of the study and the automated system results. None of the estimated frequencies was significantly different between manual and automated methods, regardless of whether individual slides or pooled results across all samples were compared. To our knowledge, this is the first report examining the validity of automated cell scoring in human spermatozoa. The results from this pilot exploration of sperm FISH suggest the comparability between automated and manual methods for estimating sex chromosome disomy and provide evidence that automated laser scanning of multiprobe sperm FISH should be explored further.

Establishment and study of different real-time polymerase chain reaction assays for the quantification of cells with deletions of chromosome 7

The evaluation of residual disease, which has prognostic value in the treatment of hematological malignancies, is currently assessed by scoring a limited number of cells by karyotyping and molecular cytogenetics. Real-time polymerase chain reaction (PCR) is an easier and more sensitive technique, enables analysis of a larger number of cells, and decreases sampling error. However, real-time PCR has been applied only to target transcripts of fusion genes. Here, we considered two real-time PCR strategies to quantify a number of cells carrying a partial deletion of chromosome 7 mixed with normal disomic cells. The first strategy was based on the amplification of two sequences, one on chromosome 7 and the other on chromosome 14. In the second strategy residual disease was assessed by the ratio between the two alleles of a bi-allelic marker, mapped on chromosome 7, measured with allele-specific assays. Precision and accuracy of the two approaches were tested by reference samples with nominal values of residual disease ranging from 2 to 95%. As expected the second strategy resulted in more precise and accurate monitoring within the range from 5 to 95%. Furthermore, this method may be applied to assess the number of dysplastic or neoplastic clones carrying any unbalanced chromosome changes.

Sensitive detection of tumour cells in effusions by combining cytology and fluorescence in situ hybridisation (FISH)

Diagnosis of malignant cells in effusions is important for staging procedures and resulting therapeutic decisions. Cytodiagnostics in effusions is sometimes difficult since reactive mesothelial cells can mimic malignant cells. We used fluorescence in situ hybridisation (FISH) in single-colour or if appropriate in dual-colour evaluation to detect chromosomal aberrations in effusion cells as markers of malignancy, to raise the diagnostic yield. Cytologic and FISH evaluations – by using probes representing several chromosomes always including chromosomes 11 and 17 – were performed in 358 effusion fluids. Cytology was positive for malignancy in 44.4% of all effusions, whereas FISH was positive in 53.9% (P=0.0001). The combination of cytology and FISH was diagnostic for malignancy in 60.9% of effusions. Diagnostic superiority of FISH was demonstrated in effusions from breast cancer, lung cancer, pancreatic cancer, and in effusions from the entire group of gynaecological and gastrointestinal carcinomas. In transudates (effusion protein <2.5 g dl⁻¹), malignant cells were detectable by cytology, FISH, and combined use of both methods in 18.6, 30, and 37.1% of effusions, respectively, suggesting that cytologic and molecular analysis should be performed also with transudates. In conclusion, FISH in combination with conventional cytology is a highly sensitive and specific diagnostic tool for detecting malignant cells in effusions.

Determination of cutoff values to detect small aneuploid clones by interphase fluorescence in situ hybridization: the Poisson model is a more appropriate approach. Should single-cell trisomy 8 be considered a clonal defect?

We applied a dual-color interphase in situ fluorescence hybridization (I-FISH) technique using centromeric probes specific to chromosomes 7 and 8 on 20 control samples in order to define the statistical model best suited to determine cutoff values for detection of small abnormal clones. We found that the Poisson model is a more appropriate approach than a Gaussian model. Then, based on the analysis of 91 samples from 80 patients with myelocytic malignant hemopathies and either clonal or nonclonal -7 or +8 as determined with conventional cytogenetics (CC), we compared the respective power of I-FISH and CC for detection of aneuploidy, with special emphasis on the potential contribution of I-FISH as a complement to CC in the case of small abnormal clones. The I-FISH results were positive in samples with clonal -7 or +8 according to CC analysis. Whereas I-FISH was negative in samples with nonclonal -7 according to CC, thus confirming the reliability of the criteria used to define the clonality of -7; the situation was different with nonclonal +8. I-FISH revealed the clonality of +8 in most samples with single-cell +8. In several cases, however, the unquestionable clonal nature of +8, as evidenced during follow-up, could not be established with either CC or I-FISH according to accepted criteria. Our data suggest that, in case of a single metaphase with +8, the general rule should be amended and the single-cell +8 should be considered and reported as potentially clonal.

Effect of exercise on stability of chronically enlarged motor units

Chronic denervation syndromes such as the post-polio syndrome are associated with progressive muscle weakness and fatigue after motoneuron death. Neither the etiology nor the management of these syndromes is clear. To address this issue, we partially denervated rat hindlimb muscles for 1 or 12 months and examined whether chronically enlarged motor units (MUs) become destabilized with time and further destabilized by daily running on exercise wheels. MU enlargement, measured electrophysiologically and morphologically was significantly reduced at 12 months in extensively denervated muscles, and to a lesser extent in moderately denervated muscles, as compared to the findings at 1 month. A 1-month period of running exercise further reduced the size of the chronically enlarged MUs in the extensively denervated muscles. We have therefore (1) successfully established a rat model of time-related MU size reduction, in which destabilization of chronically enlarged MUs results in loss of axonal terminals, and (2) demonstrated that nonphysiological activity has small but significant effects of further destabilizing the chronically enlarged MUs.

Malignant cell detection by fluorescence in situ hybridization (FISH) in effusions from patients with carcinoma

Cytological diagnosis of malignant cells in effusions is hampered by difficulties in the differentiation from reactive mesothelial cells. Because interphase cytogenetics by fluorescence in situ hybridization (FISH) might complement cytological evaluation, we determined the power of tumor cell detection using FISH and cytology in 201 effusions from patients with advanced cancer. Furthermore, 9 primary breast tumors were FISH-karyotyped, and chromosomal aberrations were compared with those of corresponding metastatic effusion cells. By using centromeric probes representing chromosomes 7, 8, 11, 12, 17, and 18, a rate of malignancy-associated aneusomy combined for the 6 chromosomes was detected in an overall of 44.8% of effusion specimens (range, 31.8% to 39.3% for the individual chromosome), comparable to cytology (43.3%). The combination of just 2 FISH probes (namely, representing chromosome pairs 8/11 and 8/17) was almost equally efficient in the identification of aneusomy. Approximately one fourth of the cytologically negative effusions were FISH positive and vice versa. From the initially FISH-negative effusions, 18.9% could be subsequently classified positive with dual-color FISH by visualization of intranuclear chromosomal complexity in rare aneuploid cells. Thus, "overall FISH analysis," including dual-color evaluation, identified tumor cells in significantly more effusions (55.2%, P = .001) than conventional cytology, implying greater sensitivity. Finally, our finding that numerical aberration patterns in primary breast tumors and corresponding metastatic effusions are comparable indicates that FISH examination of primary tumors will indicate the centromeric probe(s) best suited for an efficient search for metastasis in the individual case.

Hyperdiploidy and apparent aneusomy in mesothelial cells from non-malignant effusions as detected by fluorescence in situ hybridization (FISH)

Interphase cytogenetics by fluorescence in situ hybridization (FISH) can be used to detect malignant cells characterized by chromosomal aneuploidy. However, apparent aneusomy in normal "control" tissues has to be considered when using FISH as diagnostic tool. In effusions as model tissue exposed to metastasis, the definition of cut-off levels for background aneusomy by FISH was aimed in this study. Using centromeric probes representing chromosomes 7, 8, 11, 12, 17 and 18, extensive chromosome copy number enumeration by single-color FISH analysis was performed in pleural and ascitic effusions derived from 15 patients with various, non-malignant diseases. In all effusions, cells with gain of hybridization signals for several or all chromosomes tested were found (in up to 1.94% of cells). A consistent finding was high grade hyperdiploidy (>4 centromeric signals). Mesothelial elements mainly contributed to hyperdiploidy in effusions, as demonstrated by a combined analysis of FISH and immunocytochemistry with staining for cytokeratin. Dual-color FISH analysis showed that hyperdiploidy was predominantly corresponding to polyploidization; however, there were always minor cell populations classified as aneuploid by dual-color FISH. In conclusion, stringent criteria have to be applied to distinguish malignancy-related aneuploidy from background aneusomy by FISH.

Interphase cytogenetics of chromosomes 11 and 17 in fine needle aspirates of breast cancer

The aims of this investigation were to compare quantitative with qualitative analysis of fluorescent in situ hybridization (FISH) centromere signals in interphase breast cancer cell nuclei and to evaluate the possible clinical utility of detecting numerical abnormalities of chromosomes 11 and 17 by FISH in the preoperative prediction of breast cancer histological grade. Commercial digoxigenin-labeled centromere probes to chromosomes 11 and 17 were hybridized to 69 malignant aspirates with histological follow-up. Aspirates were categorized as disomic or aneusomic for chromosomes 11 and 17 qualitatively; a subset of aspirates was also analyzed quantitatively. The quantitative and qualitative approaches resulted in almost identical categorisation. There was a significant association between the qualitative categorization of aspirates as aneusomic or disomic, the histological grade of the excised tumours (P = .0695, n = 69), and the cytological grade of the clinical aspirates (P = .006, n = 35). Although histological grade III tumors were almost invariably polysomic for one or both chromosomes, polysomy was also detected in grade I and II tumors. Qualitative FISH analysis was shown to be more sensitive than cytological grading in predicting histological grade III but was of lower specificity and was therefore not clinically useful.

Validation of primed in situ labeling (PRINS) for interphase analysis: comparative studies with conventional fluorescence in situ hybridization and chromosome analyses

Primed in situ labeling (PRINS) is a rapidly developing new technology with wide ranging clinical applications. To assess the sensitivity, specificity, and accuracy of PRINS, we carried out a retrospective study on cultured bone marrow cells to detect aneuploidy for chromosomes 7, 8, and 12. The results were then compared to the results of previous fluorescence in situ hybridization (FISH) and chromosome analyses (CA). In patients who showed aneuploidy with CA, both FISH and PRINS confirmed the aneuploidy in interphase cells. FISH and PRINS also showed excellent correlation with conventional cytogenetic analysis for the detection of mosaic aneuploidies. However, both FISH and PRINS showed significantly higher sensitivity in the detection of abnormal clones compared to CA. In 9 of the 17 cases, there were no significant differences in the detection rates between the two methods. Based on our studies, we conclude that PRINS is as sensitive as FISH in most cases for aneuploidy detection; and that PRINS, like FISH, is more sensitive than conventional CA for aneuploidy detection.

Aneuploidy of chromosome 8 as detected by interphase fluorescence in situ hybridization is a recurrent finding in primary and metastatic breast cancer

Previous work from our laboratory demonstrated aneuploidy for several chromosomes by interphase fluorescence in situ hybridization (FISH) in a high proportion of breast cancer specimens. In the literature, only limited data are available concerning chromosome 8 anomalies in breast cancer. To determine chromosome 8 ploidy status in primary and metastatic specimens from 81 breast cancer patients, FISH analysis with a DNA probe recognizing chromosome 8 centromeres was performed. In all primary tumor specimens (n = 30), significant proportions of cells were aneuploid exhibiting gain of chromosome 8 copy numbers; in 75% of effusion specimens previously classified as malignant by cytology and/or FISH for various chromosomes (n = 40), cell populations aneuploid for chromosome 8 were detected; effusions previously classified non-malignant (n = 11) were diploid in 10 cases, whereas one specimen contained rare hyperdiploid cells. Among these cells complex chromosomal aneuploidy could be demonstrated by two-color FISH, suggesting malignancy. Trisomic and tetrasomic clones were predominant in the majority of samples, but a marked intratumor cytogenetic heterogeneity was observed in most cases. Primary tumors and corresponding positive axillary lymph nodes revealed similar distributions of chromosome 8 copy numbers, analogous to previous findings with other chromosomes. This implies that, by using suitable FISH probes after examination of the respective primary tumor, an efficient search for (micro)metastasis might be feasible.

Detection of chromosomal aneuploidy by interphase fluorescence in situ hybridization in bronchoscopically gained cells from lung cancer patients

BACKGROUND

Development and progression of human malignancies involve multiple genetic changes. New techniques to distinguish neoplastic from benign diseases unequivocally with small amounts of cells as gained by bronchoscopy are needed to come closer to the goal of an early diagnosis in lung cancer.

STUDY OBJECTIVE

The aim of this study was to determine whether interphase fluorescence in situ hybridization (FISH) can be used to visualize chromosomal aberrations in bronchoscopically gained cells from lung cancer patients and could eventually become a complementary technique to conventional cytology.

METHODS

We examined 20 cancerous specimens (10 primary tumors, 10 malignant effusions) of 18 lung cancer patients by FISH with DNA probes specific for chromosomes 3, 8, 11, 12, 17, and 18. From five additional patients, endobronchial brushings and/or forceps biopsy specimens were subjected to interphase FISH analysis.

RESULTS

In all primary tumors and malignant effusions, highly aneuploid cells were detectable by FISH. Chromosomal aberrations always consisted of gains of chromosomal signal numbers, and all chromosomes were found to be aneuploid to a similar extent. Using chromosomal aneuploidy as a marker of malignancy, material obtained by bronchoscopy was then examined for the presence of malignant cells. In all specimens, evidence for malignancy was obtained by FISH, including three specimens in which cells appeared to be normal or reactively changed by cytologic criteria.

CONCLUSION

We conclude that interphase FISH is useful in detecting aneuploidy associated with malignancy in bronchoscopically gained cells that do not clearly meet the criteria of malignancy by conventional cytologic study.

Interphase fluorescence in situ hybridization improves the detection of malignant cells in effusions from breast cancer patients

In diagnostic evaluation of effusions, difficulties are encountered when atypical reactive mesothelial cells have to be differentiated from malignant cells. We tested the impact of fluorescence in situ hybridization (FISH) to identify metastatic cells in breast cancer effusions by detection of numerical chromosomal changes. Pleural and ascitic fluid samples (n=57) from 41 breast cancer patients were concomitantly evaluated by routine cytology and FISH, using centromere-specific probes representing chromosomes 7, 11, 12, 17 and 18. After setting stringent cut-off levels deduced from non-malignant control effusions (n=9), the rates of cells with true aneuploidy were determined in each effusion sample from breast cancer patients. The occurrence of aneuploid cells, as detected by FISH and indicative of malignancy, was correlated with the cytological findings. Routine cytology revealed malignancy in 60% of effusions. Using FISH, aneuploid cell populations could be observed in 94% of cytologically positive and in 48% of cytologically negative effusions, thus reverting diagnosis to malignancy. To confirm malignancy in cases with a low frequency of aneuploid cells, two-colour FISH was additionally performed and indeed showed heterogeneous chromosomal aneuploidy within single nuclei. We conclude that FISH is a valuable tool in the diagnosis of malignancy and may serve as an adjunct to routine cytological examination, as demonstrated here for breast cancer effusions.

The use of FISH with chromosome-specific repetitive DNA probes for the follow-up of leukemia patients. Correlations and discrepancies with bone marrow cytology

The use of fluorescence in situ hybridization (FISH) for the purpose of repeated follow-up examination of bone marrow samples from 38 leukemia patients was investigated. On the basis of conventional cytogenetic analysis, patients with acute leukemia whose leukemic cells carried numerical chromosomal aberrations were selected and followed with repetitive DNA probes that specifically hybridize to one chromosome type. Repeated cytogenetic metaphase analyses would have been laborious and not sensitive or quantitative enough to follow declining numbers of aberrant cells. FISH, as an interphase cytogenetic technique, provides a rapid and simple alternative with high sensitivity. Although FISH data before and after chemotherapy were in agreement with bone marrow cytology in 30 of 38 patients, discrepancies were noticed in specific cases. These could be explained by the presence of cytogenetically distinct subclones that behave differently during treatment, the presence of differentiated leukemic cells, changes in the chromosomal constitution caused by clonal relapse, or the fact that a numerical aberration is found by conventional chromosome banding analysis while the target region to which the probe is directed is still present in the nucleus as a diploid set.

Aneuploidy in breast cancer: a fluorescence in situ hybridization study

Although ploidy is associated with the development and progression of most breast cancers, the value of flow cytometric ploidy as a clinical prognostic factor remains controversial. The technique of fluorescence in situ hybridization (FISH) can be used not only to determine overall ploidy, but also to assess the over-representation or under-representation of specific chromosomes in interphase cells. This information may be of prognostic value. We studied 84 primary breast cancers and 20 metastatic tumors by FISH, using chromosome-specific fluorescent centromeric probes. Of these, 100 cases were also studied by DNA flow cytometry. The FISH studies were concordant with DNA flow cytometry with regard to distinguishing aneuploid from diploid tumors in 78% of cases. The FISH data suggested that aneuploidy arises by a process of chromosome complement doubling with subsequent chromosome loss. In tumors that exhibited evidence of more than one round of chromosome complement doubling, the selective accumulation of multiple copies of specific chromosomes or chromosome segments was common. Multiple copies of chromosomes centromeres 1, 3, and 17 were accumulated selectively in the cells of individual tumors more frequently than chromosomes centromeres 7, 11, and 16. Multiple copies of chromosomes centromeres 10 and 20 were selectively accumulated only rarely, if at all. Aneuploidy in breast cancer can be divided into distinct stages using fluorescence in situ hybridization techniques. The stages of aneuploidy provide potential landmarks in the genetic evolution of this disease with possible links to chromosome-specific evolutionary changes.

Advantages and limitations of using fluorescence in situ hybridization for the detection of aneuploidy in interphase human cells

Fluorescence in situ hybridization with chromosome-specific DNA probes is being increasingly utilized for the detection of chromosome aberrations induced in vitro and in vivo by chemical and physical agents. Although potentially a powerful technique, FISH studies for aneuploidy can be heavily influenced by cellular phenomena and hybridization artifacts which make the performance and interpretation of the results difficult. As a consequence, frequently hyperdiploid frequencies are reported in the literature which are substantially higher than one would expect based upon frequencies seen in conventional metaphase analyses. In this article, a number of the potential pitfalls that we have encountered while performing FISH analyses for aneuploidy are discussed and their potential impact on the observed hybridization frequencies is described. After considering these factors, the frequencies of lymphocyte nuclei containing 3 and 4 chromosome copies are compared between metaphase values obtained from published human population studies and interphase values obtained from similar studies using FISH. It is concluded that by using caution in the evaluation of slides, interphase studies using FISH to detect hyperdiploidy and polyploidy can provide estimates of numerical alterations which closely reflect those seen during metaphase analysis using either FISH or conventional approaches. However, due to the inability of interphase analysis to distinguish hyperdiploidy from polyploidy as well as other potential problems, frequencies of aneuploid nuclei obtained using single label FISH should only be considered approximations of absolute frequencies. For additional accuracy, multi-color FISH with two or more different probes should be performed.

Heterogeneity of lineage involvement by trisomy 8 in myelodysplastic syndrome. A multiparameter analysis combining conventional cytogenetics, DNA in situ hybridization, and bone marrow culture studies

To better understand the role of trisomy 8 in myelodysplastic syndrome (MDS), we performed a multiparameter analysis combining conventional chromosome studies (CCS), fluorescence in situ hybridization (FISH), and bone marrow (BM) culture studies in two patients with MDS evolving into acute myeloid leukemia (AML). A mosaicism of a cytogenetically normal clone and a clone with trisomy 8 was detected in both patients throughout the course of the disease, a finding confirmed by FISH on BM cells. The relative size of the trisomic clone increased from 52% to 71% (p < 0.0001) and from 53% to 69% (p = 0.001) of all BM cells at the time of the leukemic switch in patients 1 and 2, respectively. Combined FISH and immunophenotyping of BM cells showed involvement of the granulomonocytic lineage in patient 1 and involvement of erythroid cells as well as of the granulomonocytic lineage in patient 2. Only disomic lymphocytes were detected in both patients. FISH on single hemopoietic colonies grown in semisolid media detected trisomic CFU-GM and disomic BFU-E in patient 1, whereas a proportion of CFU-GM and BFU-E deriving from the trisomic clone was detected in patient 2. However, the percent of trisomic colonies was lower than the percent of involved granulomonocyte precursors and involved erythroblasts, as detected by combined FISH and immunophenotyping on fresh BM samples. We have thus shown heterogeneity of lineage involvement by trisomy 8 in MDS undergoing transformation into AML. Although preferential growth of disomic clones may occur in vitro, the finding of an increased size of the trisomic clone at the time of leukemic switch suggests that these cells had proliferative advantage in vivo over cells without trisomy 8.

Interphase cytogenetics reveals a high incidence of aneuploidy and intra-tumour heterogeneity in breast cancer

The occurrence of aberrations involving chromosomes 11 and 17 in malignant tissues of breast cancer patients has not yet been studied systematically. Using fluorescence in situ hybridisation (FISH) with centromere-specific probes, we determined chromosome 11 and 17 status in interphase nuclei from primary and/or metastatic breast cancer cells. In all cancerous specimens obtained from 30 patients, FISH identified cells with clonal chromosomal abnormalities, with aneuploidy rates ranging from 6% to 92% (median 59%). There was a gain of centromeric signals for chromosome 11, most likely corresponding to hyperploidy; aberrations of chromosome 17 in specimens from 26 patients (87%) were hyperploid as well; however, four cases (13%) showed loss of chromosome 17 centromeres. All specimens contained heterogeneous aneuploid cell populations with excessive gain of signals in some cases. The pattern of aneuploidy did not appear to correlate with tumour grade/stage and was comparable in primary tumours and corresponding metastatic axillary lymph nodes, indicative of genetic instability early in tumour development. Screening with a panel of FISH probes may lead to enhanced sensitivity and specificity in detecting malignant cells, as demonstrated in this study with effusions which could not be conclusively interpreted as being malignant by cytological criteria.

Molecular cytogenetics: unraveling of the genetic composition of individual cells by fluorescence in situ hybridization and digital imaging microscopy

Molecular biology techniques allow the unraveling of the genetic alterations that cause or accompany malignant disease. Since tumors are often heterogeneous, biochemical analysis of tissue homogenates is of limited diagnostic value. This paper gives examples of methods that are presently operational to analyze the genetic composition of individual cells. They are based on fluorescence in situ hybridization (FISH) and digital imaging microscopy. First, the current status of indirect and direct FISH staining methods with respect to probe labeling, detection sensitivity, multiplicity, and DNA resolution is summarized. Microscope hardware as well as charge-coupled device (CCD) cameras required for FISH analysis are then described. Applications potentially important for the analysis of urological malignancies, such as the automated enumeration of chromosomal abnormalities (counting of dots in interphase cells) and high-resolution DNA mapping on highly extended chromatin, are described in detail. Finally, the limitations of the present methodology and its future prospects are discussed.

Determination by interphase-FISH of the clonality of aberrant karyotypes in human hematopoietic neoplasias

Interphase-FISH (fluorescence in situ hybridization) studies have been devoted to the determination of clonality of aberrant karyotypes in human leukemia. Various levels of its extent have been examined, including the meaning of a single aberrant karyotype as representing a microclone, the use of FISH to confirm clonality in bi- or multiclonal leukemia, the estimation of the residual (aberrant) clone after contrasexual bone marrow transplantation, and the redetectability in interphase of the abl/bcr rearrangement. The quantitative findings of all these lines of interphase FISH analyses were based on the comparison with data from a large-scale "control" study on normal cells using the same DNA probes which have been chosen for the determination of clonality, i.e. centromeric DNA probes for chromosomes #1, #3, from #6 to #12, from #15 to #18, #20, X and Y, and a specific probe for the abl/bcr rearrangement. In addition, the validity of interphase-FISH analysis on classical bone marrow smears was examined. As a common outcome it was concluded that interphase-FISH technique is a valuable tool for defining clonality of karyotypic changes and, as a consequence, yields additional prognostic information in many human leukemias. It is recommended to perform interphase FISH in routine cytogenetics of leukemia, whenever reasonable.

CCD microscopy and image analysis of cells and chromosomes stained by fluorescence in situ hybridization

This paper reviews methods and applications of CCD microscopy for analysing cells and chromosomes subjected to fluorescence in situ hybridization (FISH). The current status of indirect and direct FISH staining methods with respect to probe labelling, detection sensitivity, multiplicity and DNA resolution is summarized. Microscope hardware, including special multi-band pass filters and CCD cameras required for FISH analysis, is described. Then follows a detailed discussion of current and emerging applications such as the automated enumeration of chromosomal abnormalities (counting of dots in interphase cells), comparative genomic hybridization, automated evaluation of radiation-induced chromosomal translocations, and high-resolution DNA mapping on highly extended chromatin. Finally, the limitations of the present methodology and future prospects are discussed.

Counting, measuring, and mapping in FISH-labelled cells: sample size considerations and implications for automation

Statistical models are used to investigate the need for automation in several potential areas of application of FISH-labelling techniques, including perinatal and tumour cytogenetics, genetic toxicology, and gene mapping. Predictions of the models, based on current estimates of likely error rates for spot-counting and measuring, suggest that a fully automated system is a realistic prospect for detecting full or high-level mosaic trisomies and that interactive systems have the potential to reduce substantially the human workload required to detect residual malignant disease or radiation-induced chromosome aberrations. There appear to be no foreseeable limits to the requirements for speed and accuracy in such systems, since there is effectively no lower limit to the level of relevant biological detail that can be investigated with these techniques.